Circadian rhythms are endogenous oscillations of physiological functions that occur in diverse organisms. These rhythms share many formal and biochemical properties, raising the possibility that common mechanisms underlie all circadian clocks from cyanobacteria to humans. With this theoretical framework, the original P01 grant proposed that, by using common technologies in technical cores and shared data, a common process could be studied in 4 instructive model systems: the cyanobacterium Synechococcus, the fungus Neurospora, the chick pineal gland, and the rodent suprachiasmatic nucleus (SCN). The research instead revealed that all circadian systems, from cyanobacteria to mammals and birds: (1) comprise multiple circadian oscillations that behave independently under some experimental conditions and are integrated by complex processes; (2) regulate intermediary metabolism and redox state as both downstream processes of the clock and perhaps as part of the clock mechanism itself; (3) regulate protein dynamics in terms of both protein synthesis and catabolism; and (4) incorporate post-translational regulation as the rule rather than the exception, such that transcription/translation loop models are not sufficient to explain the clock. Further, the data told us that homology of known oscillator components is not a common element: (1) The sequences of known clock genes are very different if one discounts common protein-protein interaction motifs; (2) The temporal dynamics of clock gene transcription and translation are disparate enough that a deep evolutionary relationship among these diverse model systems is unlikely. The present proposal seeks to extend these findings by placing the circadian clock in the context of these organisms' cellular machinery, metabolism, and protein dynamics. We will ask: (1) How are multiple circadian oscillatory mechanisms coordinated within and among cells?; (2) How do metabolic processes interact with clock machinery in each of these systems?; (3) How does the regulation of protein dynamics fit into the overall scheme of circadian organization?; and (4) What are the fundamentally conserved properties of the clocks among these diverse organisms? Lay summary: This research will lead the way to a comprehensive systems biology approach to biological clocks that will elucidate chronobiological disorders associated with sleep and wakefulness, many of which are attended by metabolic, endocrine, and cell-cycle disorders.